As of June 15th 2018, the Private Lodging Business Act is now in effect which places restrictions on room reservations made at unlicensed or unauthorized accommodations in Japan. Travelers can confirm if an alternative accommodation such as a guest house is registered by inquiring directly with the online booking site. There are a variety of accommodation options available in Japan beyond western style hotels such as traditional Japanese inns and guest houses which are licensed and duly registered. The link also provides a list of appropriate booking sites for such accommodations.
For more information: https://www.japan.travel/en/news/notice-about-private-lodging-in-japan/
